[gmx-users] trjconv - PBC

[Justin A. Lemkul]

Steven Neumann wrote:
> Dear Gmx Users,
>  
> I am trying to convert my trajectory using trjconv.  My system is made 
> of 10 ligands and protein. Protein is jumping 
> divided into parts. The same is with my ligands. I am confused about the 
> point 2 and 3:
>  
>  
> 
> 2. Extract the first frame from the trajectory as reference for removing 
> jumps if you want to remove jumps.
> 
>  
> 
> Which option of trjconv is responsible for extraction of my 1st frame?
> 
>  

trjconv -dump 0

> 
> 3. Remove jumps if you want to have them removed using the first frame
> 
>  
> 
> trjconv -f traj.xtc -s *.tpr -pbc nojump (how to use 1st frame here 
> extracted from previous point?)
> 
>  

Recreate the .tpr file using the coordinate file produced in (2).

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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